diff --git a/src/drift/checkers/command.ts b/src/drift/checkers/command.ts
index 04cc1d94..8d445d50 100644
--- a/src/drift/checkers/command.ts
+++ b/src/drift/checkers/command.ts
@@ -2,6 +2,77 @@ import { readFileSync, existsSync } from "node:fs";
 import { resolve } from "node:path";
 import type { Claim, DriftIssue } from "../../types.js";
 
+/**
+ * First-token verbs that yarn/pnpm treat as their own commands. Bare
+ * `yarn install` / `pnpm add` must not be looked up as package.json scripts.
+ * `run` is handled separately so `yarn run <script>` still checks scripts.
+ */
+const YARN_PNPM_BUILTINS = new Set([
+  "add",
+  "audit",
+  "bin",
+  "cache",
+  "ci",
+  "config",
+  "create",
+  "dedupe",
+  "deploy",
+  "dlx",
+  "doctor",
+  "env",
+  "exec",
+  "explain",
+  "fetch",
+  "focus",
+  "global",
+  "help",
+  "import",
+  "init",
+  "install",
+  "link",
+  "list",
+  "login",
+  "logout",
+  "ls",
+  "outdated",
+  "pack",
+  "patch",
+  "patch-commit",
+  "plugin",
+  "prune",
+  "publish",
+  "rebuild",
+  "recursive",
+  "remove",
+  "root",
+  "set",
+  "setup",
+  "store",
+  "uninstall",
+  "unlink",
+  "unset",
+  "unplug",
+  "up",
+  "update",
+  "upgrade",
+  "version",
+  "why",
+  "workspace",
+  "workspaces",
+  "i",
+  "rm",
+]);
+
+/** Resolve a package-manager invocation to a script name, or null if it is not a script lookup. */
+function packageManagerScriptName(cmd: string): string | null {
+  const scopedRun = cmd.match(/^(?:npm|yarn|pnpm|bun)\s+run\s+(\S+)/);
+  if (scopedRun) return scopedRun[1];
+
+  const bare = cmd.match(/^(?:yarn|pnpm)\s+(\S+)/);
+  if (!bare) return null;
+  return YARN_PNPM_BUILTINS.has(bare[1]) ? null : bare[1];
+}
+
 /** Check that claimed npm/yarn/make commands actually exist */
 export function checkCommands(
   claims: Claim[],
@@ -19,11 +90,8 @@ export function checkCommands(
     const cmd = claim.value.trim();
 
     // npm run <script> / yarn <script> / pnpm <script>
-    const npmMatch = cmd.match(
-      /^(?:npm\s+run|yarn|pnpm|bun\s+run)\s+(\S+)/
-    );
-    if (npmMatch) {
-      const script = npmMatch[1];
+    const script = packageManagerScriptName(cmd);
+    if (script !== null) {
       if (pkgScripts && !pkgScripts.has(script)) {
         issues.push({
           code: "DEAD_COMMAND",
diff --git a/src/drift/checkers/index-sync.ts b/src/drift/checkers/index-sync.ts
index 2a66e011..a618cda7 100644
--- a/src/drift/checkers/index-sync.ts
+++ b/src/drift/checkers/index-sync.ts
@@ -2,6 +2,11 @@ import { readFileSync, existsSync } from "node:fs";
 import { resolve, basename } from "node:path";
 import { globSync } from "glob";
 import type { DriftIssue } from "../../types.js";
+import { extractFrontmatter } from "../../markdown.js";
+
+const EDGE_TARGET_PATTERN = /(?:^|\/)patterns\/([^/]+\.md)$/;
+/** INDEX.md lives in patterns/, so sibling edge targets omit the patterns/ prefix. */
+const INDEX_SIBLING_TARGET = /^(?:\.\/)?([^/]+\.md)$/;
 
 /** Cross-reference patterns/INDEX.md with actual pattern files */
 export function checkIndexSync(projectRoot: string, scaffoldRoot: string): DriftIssue[] {
@@ -38,6 +43,22 @@ export function checkIndexSync(projectRoot: string, scaffoldRoot: string): Drift
     referencedFiles.add(match[1]);
   }
 
+  // Frontmatter edges are mex's canonical navigation, so a pattern reached
+  // only through an edge is not orphaned. Parsed from the content already
+  // read above rather than re-reading the file.
+  const edges = extractFrontmatter(rawContent)?.edges;
+  for (const edge of Array.isArray(edges) ? edges : []) {
+    const target = typeof edge?.target === "string" ? edge.target.replace(/#.*$/, "") : "";
+    if (!target) continue;
+    const fromPatterns = EDGE_TARGET_PATTERN.exec(target);
+    if (fromPatterns) {
+      referencedFiles.add(fromPatterns[1]);
+      continue;
+    }
+    const sibling = INDEX_SIBLING_TARGET.exec(target);
+    if (sibling) referencedFiles.add(basename(sibling[1]));
+  }
+
   // Check: pattern files not in INDEX
   for (const file of patternFiles) {
     if (!referencedFiles.has(file)) {
diff --git a/test/checkers.test.ts b/test/checkers.test.ts
index 6368c102..e95c81f5 100644
--- a/test/checkers.test.ts
+++ b/test/checkers.test.ts
@@ -421,6 +421,39 @@ describe("checkCommands", () => {
     const issues = checkCommands(claims, tmpDir);
     expect(issues).toHaveLength(0);
   });
+
+  it("does not treat yarn/pnpm builtins as missing scripts", () => {
+    writeFileSync(
+      join(tmpDir, "package.json"),
+      JSON.stringify({ scripts: { build: "tsc" } })
+    );
+    const claims = [
+      claim({ kind: "command", value: "pnpm install" }),
+      claim({ kind: "command", value: "yarn add" }),
+      claim({ kind: "command", value: "pnpm dlx" }),
+      claim({ kind: "command", value: "yarn ci" }),
+    ];
+    expect(checkCommands(claims, tmpDir)).toHaveLength(0);
+  });
+
+  it("still reports a missing yarn/pnpm script", () => {
+    writeFileSync(
+      join(tmpDir, "package.json"),
+      JSON.stringify({ scripts: { build: "tsc" } })
+    );
+    const issues = checkCommands(
+      [
+        claim({ kind: "command", value: "pnpm lint" }),
+        claim({ kind: "command", value: "yarn run missing" }),
+      ],
+      tmpDir
+    );
+    expect(issues).toHaveLength(2);
+    expect(issues.map((issue) => issue.message)).toEqual([
+      'Script "lint" not found in package.json scripts',
+      'Script "missing" not found in package.json scripts',
+    ]);
+  });
 });
 
 // ── Dependency Checker ──
@@ -738,6 +771,31 @@ describe("checkIndexSync", () => {
     const issues = checkIndexSync(tmpDir, tmpDir);
     expect(issues).toHaveLength(0);
   });
+
+  it("treats a frontmatter edge as an INDEX reference", () => {
+    mkdirSync(join(tmpDir, "patterns"), { recursive: true });
+    writeFileSync(
+      join(tmpDir, "patterns/INDEX.md"),
+      "---\nedges:\n  - target: syntax-extractor-review.md\n---\n\n# Index\n"
+    );
+    writeFileSync(join(tmpDir, "patterns/syntax-extractor-review.md"), "# Review");
+    const issues = checkIndexSync(tmpDir, tmpDir);
+    expect(issues).toHaveLength(0);
+  });
+
+  it("still reports a pattern with no INDEX link or edge", () => {
+    mkdirSync(join(tmpDir, "patterns"), { recursive: true });
+    writeFileSync(
+      join(tmpDir, "patterns/INDEX.md"),
+      "---\nedges:\n  - target: syntax-extractor-review.md\n---\n\n# Index\n"
+    );
+    writeFileSync(join(tmpDir, "patterns/syntax-extractor-review.md"), "# Review");
+    writeFileSync(join(tmpDir, "patterns/orphan.md"), "# Orphan");
+    const issues = checkIndexSync(tmpDir, tmpDir);
+    expect(issues).toHaveLength(1);
+    expect(issues[0].code).toBe("INDEX_MISSING_ENTRY");
+    expect(issues[0].message).toContain("patterns/orphan.md");
+  });
 });
 
 // ── Stale Pattern Checker ──